Closed davidvilanova closed 1 month ago
Hi, i have gone through the isoseq pipeline (using latest isoseq version).
isoseq 4.0.0 (commit v4.0.0) Using: pbbam : 2.4.99 (commit v2.4.0-16-g5cc6e4b) pbcopper : 2.3.99 (commit v2.3.0-14-g5ac5693) pbmm2 : 1.11.99 (commit v1.11.0-1-g1b5a417) minimap2 : 2.15 parasail : 2.1.3 boost : 1.77 htslib : 1.17 zlib : 1.2.13
pigeon 1.2.0 (commit -v1.2.0) Using: pbbam : 2.5.0 (commit v2.5.0) pbcopper : 2.4.0 (commit v2.4.0) boost : 1.76 htslib : 1.17 zlib : 1.2.11
When classifying the transcripts using pigeon classify i get this error:
pigeon classify -j ${CPUS} --fl ${collapse}/${part}.isoform.flnc_count.txt --log-file ${classification}/${part}.log --cage-peak ${tss} --out-dir ${classification} ${collapse}/${part}.isoform.sorted.gff ${gtf} ${genomefa}
| 20240229 09:22:59.986 | WARN | Skipping reference (MU273394.1) - missing from CAGE peak data | 20240229 09:22:59.986 | WARN | Skipping reference (MU273395.1) - missing from reference annotations | 20240229 09:22:59.986 | WARN | Skipping reference (MU273395.1) - missing from CAGE peak data | 20240229 09:22:59.986 | WARN | Skipping reference (MU273397.1) - missing from reference annotations | 20240229 09:22:59.986 | WARN | Skipping reference (MU273397.1) - missing from CAGE peak data | 20240229 09:23:22.665 | FATAL | pigeon classify ERROR: invalid BED line: 66 rfhg_2.1 1 -
This the header of my cage-peak bed file:
bed file: refTSS_v4.1_human_coordinate.hg38.bed [](coming from https://reftss.riken.jp/datafiles/current/human/)
chr1 16013 16020 rfhg_1.1 1 - chr1 29346 29366 rfhg_2.1 1 - chr1 36521 36538 rfhg_3.1 1 +
Please let us know if you still have this error. Closing until then. Looks like an issue with your bed.
Hi, i have gone through the isoseq pipeline (using latest isoseq version).
When classifying the transcripts using pigeon classify i get this error:
pigeon classify -j ${CPUS} --fl ${collapse}/${part}.isoform.flnc_count.txt --log-file ${classification}/${part}.log --cage-peak ${tss} --out-dir ${classification} ${collapse}/${part}.isoform.sorted.gff ${gtf} ${genomefa}
This the header of my cage-peak bed file:
bed file: refTSS_v4.1_human_coordinate.hg38.bed [](coming from https://reftss.riken.jp/datafiles/current/human/)